alakazam (version 1.5.0)

seqMismatchCount: Count or locate mismatches between sample and germline sequences

Description

seqMismatchCount counts Hamming-style mismatches between paired sample and germline sequences, seqMismatchMatrix counts them between every sample and every germline, and seqMismatchPositions returns the mismatch positions of paired sequences.

Usage

seqMismatchCount(
  samples,
  germlines,
  ignore = c("N", "-", ".", "?"),
  count_trailing = FALSE
)
seqMismatchMatrix(
  samples,
  germlines,
  ignore = c("N", "-", ".", "?"),
  count_trailing = FALSE
)
seqMismatchPositions(
  samples,
  germlines,
  ignore = c("N", "-", ".", "?"),
  count_trailing = FALSE
)

Value

seqMismatchCount: an integer vector of mismatch counts.

seqMismatchMatrix: an integer matrix of mismatch counts, samples in rows and germlines in columns.

seqMismatchPositions: a list of integer vectors of 1-based mismatch positions.

Arguments

samples

character vector of sample sequences.

germlines

character vector of germline sequences. For seqMismatchCount and seqMismatchPositions, a single germline is recycled across all samples.

ignore

vector of characters to ignore, in either sequence. Default is to ignore c("N", "-", ".", "?").

count_trailing

if TRUE, sample positions past the end of a shorter germline count as mismatches, so a germline gains nothing from ending early. If FALSE, sequences are compared only through the length of the shorter one.

Details

Comparisons are case-insensitive. A missing (NA) sample or germline gives NA.

Examples

seqMismatchCount(c("ATGGC", "ATGGN"), "ATGGC")
seqMismatchMatrix(c("ATGGC", "ATGGN"), c("ATGGC", "ATGGG"))
seqMismatchPositions("ATGGCA", "ATGG")

# A germline that ends early is not rewarded for it
seqMismatchMatrix("ATGGCA", c(full="ATGGCC", short="ATGG"))
seqMismatchMatrix("ATGGCA", c(full="ATGGCC", short="ATGG"), count_trailing=TRUE)